Bioinformatics and computational biology play a critical role in bioscience and biomedical research. As researchers design their experimental projects, one major challenge is to find the most relevant bioinformatics toolkits that will lead to new knowledge discovery from their data. The Bio-TDS (BioQuery Tools Discovery Systems, http://brin.usd.edu/BioQueryTool/) has been developed to assist researchers in retrieving the most applicable analytic tools by allowing them to formulate their questions as free text. The Bio-TDS is a flexible retrieval system that affords users from multiple bioscience domains (e.g. genomic, proteomic, bio-imaging) the ability to query over 12,000 analytic tool descriptions integrated from well-established, community repositories.  One of the primary components of the Bio-TDS system is the ontology and natural language processing workflow for annotation, curation, query processing, and evaluation. The Bio-TDS’s scientific impact was evaluated using sample questions posed by researchers retrieved from Biostars, a site focusing on biological data analysis. The Bio-TDS was compared to five similar bioscience analytic tool retrieval systems with the Bio-TDS outperforming the others in terms of relevance and completeness.  The Bio-TDS offers researcher the capacity to associate their bioscience question with the most relevant computational toolsets required for the data analysis in their knowledge discovery process.